195d8eff01e3453a9027c0b679c68410e197f3c7 gperez2 Fri Jul 31 13:58:07 2026 -0700 Adding release tags to the gnomadVariantsV4.1 composite and its gnomadExomesVariantsV4_1/gnomadGenomesVariantsV4_1 subtracks. refs #37351 diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.ra src/hg/makeDb/trackDb/human/hg38/gnomad.ra index e181c49c615..39cb46d815a 100644 --- src/hg/makeDb/trackDb/human/hg38/gnomad.ra +++ src/hg/makeDb/trackDb/human/hg38/gnomad.ra @@ -120,30 +120,31 @@ html gnomadV3.html track gnomadVariantsV4.1 parent gnomadVariants compositeTrack on shortLabel gnomAD v4.1.1 longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1.1 type bigBed 9 + configureByPopup off maxWindowCoverage 200000 maxItems 50000 dataVersion Release v4.1.1 (March 30, 2026) html gnomadV4.1 priority 1 visibility squish + release alpha track gnomadExomesVariantsV4_1 parent gnomadVariantsV4.1 on visibility squish shortLabel gnomAD v4.1.1 Exomes longLabel Genome Aggregation Database (gnomAD) Exomes Variants v4.1.1 dataVersion Release v4.1.1 (March 30, 2026) type bigBed 9 + itemRgb on searchIndex name,_displayName,rsId html gnomadV4.1 bigDataUrl /gbdb/hg38/gnomAD/v4.1.1/exomes/exomes.bb priority 2 labelFields rsId,_displayName defaultLabelFields _displayName @@ -151,30 +152,31 @@ skipEmptyFields on filterValues.annot pLoF,missense,synonymous,other filterValuesDefault.annot pLoF,missense,synonymous filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only) filterType.FILTER multipleListAnd filterValuesDefault.FILTER PASS filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation filterType.variation_type multipleListOr filter.AF 0.0 filterLabel.AF Minor Allele Frequency Filter mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd} ($ref/$alt)<br> <b>TotalAF</b>: ${AF} (${AC}/${AN})<br> <b>Genes</b>: $genes<br> <b>Annotation</b>: $annot<br> <b>FILTER</b>: ${FILTER}<br> <b>PopMaxAF</b>: ${grpmax}<br> <b>Homozygous Individuals</b>: ${nhomalt}<br> <b>Hemizygous Individuals (only in chrX & chrY)</b>: ${nhemi} url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r4 urlLabel View this variant at gnomAD detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1.1/exomes/gnomad.v4.1.1.exomes.details.tab.gz + release alpha track gnomadGenomesVariantsV4_1 parent gnomadVariantsV4.1 on visibility squish shortLabel gnomAD v4.1.1 Genomes longLabel Genome Aggregation Database (gnomAD) Genome Variants v4.1.1 dataVersion Release v4.1.1 (March 30, 2026) type bigBed 9 + itemRgb on searchIndex name,_displayName,rsId html gnomadV4.1 bigDataUrl /gbdb/hg38/gnomAD/v4.1.1/genomes/genomes.bb priority 1 labelFields rsId,_displayName defaultLabelFields _displayName @@ -182,30 +184,110 @@ skipEmptyFields on filterValues.annot pLoF,missense,synonymous,other filterValuesDefault.annot pLoF,missense,synonymous filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only) filterType.FILTER multipleListAnd filterValuesDefault.FILTER PASS filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation filterType.variation_type multipleListOr filter.AF 0.0 filterLabel.AF Minor Allele Frequency Filter mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd} ($ref/$alt)<br> <b>TotalAF</b>: ${AF} (${AC}/${AN})<br> <b>Genes</b>: $genes<br> <b>Annotation</b>: $annot<br> <b>FILTER</b>: ${FILTER}<br> <b>PopMaxAF</b>: ${grpmax}<br> <b>Homozygous Individuals</b>: ${nhomalt}<br> <b>Hemizygous Individuals (only in chrX & chrY)</b>: ${nhemi} url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r4 urlLabel View this variant at gnomAD detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1.1/genomes/gnomad.v4.1.1.genomes.details.tab.gz + release alpha + + track gnomadVariantsV4.1 + parent gnomadVariants + compositeTrack on + shortLabel gnomAD v4.1 + longLabel Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1 + type bigBed 9 + + configureByPopup off + maxWindowCoverage 200000 + maxItems 50000 + dataVersion Release v4.1 (April 19, 2024) + html gnomadV4.1 + priority 1 + visibility squish + release beta,public + + track gnomadExomesVariantsV4_1 + parent gnomadVariantsV4.1 on + visibility squish + shortLabel gnomAD v4.1 Exomes + longLabel Genome Aggregation Database (gnomAD) Exomes Variants v4.1 + dataVersion Release v4.1 (April 19, 2024) + type bigBed 9 + + itemRgb on + searchIndex name,_displayName,rsId + html gnomadV4.1 + bigDataUrl /gbdb/hg38/gnomAD/v4.1/exomes/exomes.bb + priority 2 + labelFields rsId,_displayName + defaultLabelFields _displayName + skipFields _displayName + skipEmptyFields on + filterValues.annot pLoF,missense,synonymous,other + filterValuesDefault.annot pLoF,missense,synonymous + filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only) + filterType.FILTER multipleListAnd + filterValuesDefault.FILTER PASS + filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation + filterType.variation_type multipleListOr + filter.AF 0.0 + filterLabel.AF Minor Allele Frequency Filter + mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd} ($ref/$alt)<br> <b>TotalAF</b>: ${AF} (${AC}/${AN})<br> <b>Genes</b>: $genes<br> <b>Annotation</b>: $annot<br> <b>FILTER</b>: ${FILTER}<br> <b>PopMaxAF</b>: ${grpmax}<br> <b>Homozygous Individuals</b>: ${nhomalt}<br> <b>Hemizygous Individuals (only in chrX & chrY)</b>: ${nhemi} + url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r4 + urlLabel View this variant at gnomAD + detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies + detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1/exomes/gnomad.v4.1.exomes.details.tab.gz + release beta,public + + track gnomadGenomesVariantsV4_1 + parent gnomadVariantsV4.1 on + visibility squish + shortLabel gnomAD v4.1 Genomes + longLabel Genome Aggregation Database (gnomAD) Genome Variants v4.1 + dataVersion Release v4.1 (April 19, 2024) + type bigBed 9 + + itemRgb on + searchIndex name,_displayName,rsId + html gnomadV4.1 + bigDataUrl /gbdb/hg38/gnomAD/v4.1/genomes/genomes.bb + priority 1 + labelFields rsId,_displayName + defaultLabelFields _displayName + skipFields _displayName + skipEmptyFields on + filterValues.annot pLoF,missense,synonymous,other + filterValuesDefault.annot pLoF,missense,synonymous + filterValues.FILTER PASS,InbreedingCoeff,RF,AC0,AS_VQSR,indel_stack (chrM only),npg (chrM only) + filterType.FILTER multipleListAnd + filterValuesDefault.FILTER PASS + filterValues.variation_type 3_prime_UTR_variant,5_prime_UTR_variant,NMD_transcript_variant,coding_sequence_variant,frameshift_variant,incomplete_terminal_codon_variant,inframe_deletion,inframe_insertion,intron_variant,mature_miRNA_variant,missense_variant,non_coding_transcript_exon_variant,non_coding_transcript_variant,protein_altering_variant,splice_acceptor_variant,splice_donor_variant,splice_region_variant,start_lost,start_retained_variant,stop_gained,stop_lost,stop_retained_variant,synonymous_variant,transcript_ablation + filterType.variation_type multipleListOr + filter.AF 0.0 + filterLabel.AF Minor Allele Frequency Filter + mouseOver <b>Position</b>: $chrom:${chromStart}-${chromEnd} ($ref/$alt)<br> <b>TotalAF</b>: ${AF} (${AC}/${AN})<br> <b>Genes</b>: $genes<br> <b>Annotation</b>: $annot<br> <b>FILTER</b>: ${FILTER}<br> <b>PopMaxAF</b>: ${grpmax}<br> <b>Homozygous Individuals</b>: ${nhomalt}<br> <b>Hemizygous Individuals (only in chrX & chrY)</b>: ${nhemi} + url https://gnomad.broadinstitute.org/variant/$s-$<_startPos>-$<ref>-$<alt>?dataset=gnomad_r4 + urlLabel View this variant at gnomAD + detailsDynamicTable _jsonVep|Variant Effect Predictor,_jsonPopTable|Population Frequencies,_jsonHapTable|Haplotype Frequencies + detailsTabUrls _dataOffset=/gbdb/hg38/gnomAD/v4.1/genomes/gnomad.v4.1.genomes.details.tab.gz + release beta,public track gnomadConstraint parent gnomadVariants on shortLabel gnomAD Mut Constraint longLabel Gnocchi: Genome Aggregation Database (gnomAD) non-coding constraint of haploinsufficient variation, includes chrX bigDataUrl /gbdb/hg38/gnomAD/mutConstraint/mutConstraint.bw type bigWig setColorWith /gbdb/hg38/gnomAD/mutConstraint/mutConstraint.color.bb windowingFunction minimum altColor 0,150,0 color 150,0,0 maxHeightPixels 128:40:8 viewLimitsMax -3:3 autoScale on priority 10